An international team of microbiologists and genomicists, led by the DOE Joint Genome Institute (JGI), has invented a genetic engineering tool to simplify the study of secondary metabolites produced by microbes. These compounds mediate internal and external messaging, self-defense, and chemical warfare, and are the basis for hundreds of valuable agricultural, industrial, and medical products. The tool, called CRAGE, will help fill significant gaps in our understanding of how microbes interact with their surroundings and evolve.
The ability to produce secondary metabolites is encoded by groups of genes called biosynthetic gene clusters (BGCs) which can be passed back and forth among closely or distantly related microbes through horizontal gene transfer. In the wild, this mechanism allows microbes to adapt to changing conditions by quickly gaining or losing traits. And because this frequent swapping introduces mutations, horizontal gene transfer of BGCs drives the development of diverse compounds.
But in the artificial environment of the lab, microbes face little hardship or competition, so they typically don’t bother making these compounds. CRAGE, an acronym for chassis-independent recombinase-assisted genome engineering, is a highly efficient means of transplanting BGCs originating from one organism into many different potential production hosts simultaneously. This enables researchers to identify microbial strains that are naturally capable of producing the secondary metabolite under laboratory conditions.
More broadly, by providing a technique to transfer microbial machinery from one species to another, CRAGE will enable scientists to go beyond theories and predictions and finally observe how compounds relegated to the category of “biological dark matter” actually work. “Looking beyond secondary metabolites, CRAGE can be used to engineer microbes for the production of proteins, RNAs, and other molecules with a huge range of applications,” said Jing Ke, a scientific engineering associate at JGI and co-first author on the paper published in Nature Microbiology.
So far, Gaoyan Wang and Zhiying Zhao, the other two co-first authors, have successfully transferred BGCs into 30 diverse bacterial strains, and expect that it should work in many others, though the technique will likely need to be adapted for some species. Further research and product development are currently underway, but the technique is now available to research teams who utilize JGI (a DOE Office of Science User Facility) through pilot programs.
The work was a collaboration with Goethe University Frankfurt and DOE Environmental Molecular Sciences Laboratory (EMSL).
Read more in the Berkeley Lab News Center.